docs(docs): add installation page to manual. fix hyperlinks in index.md

improve docs

docs/mkdocs.yml

@@ -28,6 +28,7 @@ docs_dir: 'build'
 pages:
 - Home: index.md
 - VIVA Manual:
+  - Installation and Setup: installation.md
   - Filtering Your VCF File: filtering_vcf.md
   - Making Plots: plotting.md
   - Examples: examples.md

docs/src/index.md

@@ -82,7 +82,8 @@ Use the following steps to use the VIVA Jupyter Notebook utility:
 
 ## Continue reading for:
 
-* [Variant and Sample Selection](https://github.com/compbiocore/VariantVisualization.jl/tree/master/docs/src/filtering_vcf.md)
+* [Variant and Sample Selection](https://compbiocore.github.io/VariantVisualization.jl/stable/filtering_vcf/)
+
+* [Plotting Options](https://compbiocore.github.io/VariantVisualization.jl/stable/plotting/)
 
-* [Plotting Options](https://github.com/compbiocore/VariantVisualization.jl/tree/master/docs/src/plotting.md)
 

docs/src/installation.md

@@ -1,36 +1,57 @@
 #Installation
 
-##Install Julia v1.1.0
+### Install Julia v1.1.0
 Download [Julia]("https://julialang.org/downloads/")
 
-##Install the VariantVisualization.jl
-Add `VariantVisualization.jl` at the package prompt in the Julia v1.1 REPL.
+### Supported Operating Systems:
 
-```
-julia
+#### macOS 
 
-*press the ']' key to enter the package prompt*
+Sierra, High Sierra, and Mojave.
 
-(v1.1) pkg> add VariantVisualization
+#### Windows
 
-```
+Windows 10, Windows 7
 
-If successful, `VariantVisualization.jl` will be installed in your Julia packages directory (.julia/packages/) and VIVA command line tool should install with this. Adding `VariantVisualization.jl` runs a script to create an alias for the command line tool script in the bash shell. This allows the user to call VIVA from any directory.
+### Command Line Tool
 
+1. Add VariantVisualization.jl using Pkg in the Julia REPL:
+	a. run `using Pkg`
+	b. run `Pkg.clone("https://github.com/compbiocore/VariantVisualization.jl")`
+	c. run `Pkg.instantiate()`
+2. Download the [VIVA](https://github.com/compbiocore/VariantVisualization.jl/blob/master/viva) tool script and save it to a working directory for your analysis.
+3. Navigate to your working directory and follow the [VIVA manual](https://compbiocore.github.io/VariantVisualization.jl/latest/) to generate your plots.
 
-##Install the Jupyter Notebook
+### Jupyter Notebook
 
-If you plan to use the Jupyter Notebook VIVA utility, install Jupyter then download the [VIVA Notebook]().
+1. [Install Jupyter](https://jupyter.org/install)
+2. Download the [VIVA Jupyter Notebook](https://github.com/compbiocore/VariantVisualization.jl/blob/master/VIVA.ipynb).
+3. Follow the in-notebook instructions to generate your plots.
 
-If you already have Jupyter installed, update following [these instructions](https://jupyter.readthedocs.io/en/latest/projects/upgrade-notebook.html)
+### Latest Features
 
+To stay up to date with cutting edge development features install VariantVisualization.jl from the Master branch. 
 
-##New Features
-To stay up to date with new features before official version release, please check out the master branch.
+Using git from the command line:
 
 ```
-julia
+git clone https://github.com/compbiocore/VariantVisualization.jl
+```
 
+or from the Julia REPL (useful if using the PowerShell and don't have git installed):
+
+```julia
 using Pkg
 Pkg.clone("https://github.com/compbiocore/VariantVisualization.jl")
 ```
+
+### *For Developers*
+
+VIVA Jupyter notebook and the VIVA the command line tool are built with functions contained in our VariantVisualization.jl package.
+
+Developers may contribute to these open source tools by using [functions contained within VariantVisualization.jl](https://github.com/compbiocore/VariantVisualization.jl/tree/master/src/) which are carefully documented with docstrings.
+
+We have included in-line comments within the code for the [VIVA command line tool](https://github.com/compbiocore/VariantVisualization.jl/tree/master/viva).
+
+The ***VIVA Jupyter notebook*** is powered by a [main function](https://github.com/compbiocore/VariantVisualization.jl/tree/master/src/new_notebook_utils.jl) which takes arguments defined by the user in the notebook. We welcome users to post in issues to request a new feature or bug fix.
+